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Protein

U6 snRNA-associated Sm-like protein LSm2

Gene

LSM2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.8 Publications

GO - Molecular functioni

GO - Biological processi

  • mRNA splicing, via spliceosome Source: SGD
  • rRNA processing Source: UniProtKB-KW
  • tRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing, rRNA processing, tRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-28929-MONOMER.
ReactomeiREACT_294700. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm2
Alternative name(s):
Small nuclear ribonucleoprotein D homolog SNP3
Gene namesi
Name:LSM2
Synonyms:SMX5, SNP3
Ordered Locus Names:YBL026W
ORF Names:YBL0425
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome II

Organism-specific databases

CYGDiYBL026w.
EuPathDBiFungiDB:YBL026W.
SGDiS000000122. LSM2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic mRNA processing body Source: SGD
  • Lsm1-7-Pat1 complex Source: SGD
  • nucleolus Source: SGD
  • small nucleolar ribonucleoprotein complex Source: SGD
  • spliceosomal complex Source: UniProtKB-KW
  • U4/U6 x U5 tri-snRNP complex Source: SGD
  • U6 snRNP Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi35 – 351F → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication
Mutagenesisi37 – 371N → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication
Mutagenesisi63 – 631R → A: Strongly reduces affinity for poly-U RNA ends. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9595U6 snRNA-associated Sm-like protein LSm2PRO_0000125559Add
BLAST

Proteomic databases

MaxQBiP38203.
PaxDbiP38203.
PeptideAtlasiP38203.

Interactioni

Subunit structurei

Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a doughnut shape. The LSm subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Except for LSM1, where a C-terminal helix crosses the ring structure to form additional interactions with LSM3 and LSM6, each subunit interacts only with its two neighboring subunits. The LSM1-LSM7 complex interacts with PAT1; within the complex PAT1 has direct interactions with LSM2 and LSM3. Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a doughnut shape; an RNA strand can pass through the hole in the center of the ring structure. The LSm subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. A complex comprising LSM2-LSM7 without LSM1 or LSM8 may exist. Likewise, LSM2 and LSM3 can assemble into a doughnut structure that binds PAT1 (in vitro). Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
LSM1P470176EBI-180,EBI-174
LSM3P577434EBI-180,EBI-10227
LSM5P400894EBI-180,EBI-10236
LSM6Q064064EBI-180,EBI-196
LSM7P539053EBI-180,EBI-141
LSM8P470935EBI-180,EBI-313
PAT1P256444EBI-180,EBI-204

Protein-protein interaction databases

BioGridi32672. 92 interactions.
DIPiDIP-794N.
IntActiP38203. 65 interactions.
MINTiMINT-383549.

Structurei

Secondary structure

1
95
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 87Combined sources
Turni9 – 124Combined sources
Beta strandi13 – 197Combined sources
Turni20 – 223Combined sources
Beta strandi24 – 329Combined sources
Beta strandi38 – 458Combined sources
Beta strandi49 – 513Combined sources
Beta strandi54 – 585Combined sources
Beta strandi60 – 623Combined sources
Helixi64 – 663Combined sources
Beta strandi67 – 726Combined sources
Helixi74 – 763Combined sources
Helixi79 – 9315Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70B2-95[»]
4C92X-ray2.30B2-95[»]
4M75X-ray2.95B/I1-95[»]
4M77X-ray3.11B/I1-95[»]
4M78X-ray2.79B/I1-95[»]
4M7AX-ray2.78B/I1-95[»]
4M7DX-ray2.60B/I1-95[»]
4N0AX-ray3.15C/D/G1-95[»]
ProteinModelPortaliP38203.
SMRiP38203. Positions 2-95.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00390000016597.
HOGENOMiHOG000166937.
InParanoidiP38203.
KOiK12621.
OMAiDCTLLQD.
OrthoDBiEOG7PZSB0.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR016654. U6_snRNA_Lsm2.
[Graphical view]
PANTHERiPTHR13829. PTHR13829. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF016394. U6_snRNA_Lsm2. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P38203-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLFFSFFKTL VDQEVVVELK NDIEIKGTLQ SVDQFLNLKL DNISCTDEKK
60 70 80 90
YPHLGSVRNI FIRGSTVRYV YLNKNMVDTN LLQDATRREV MTERK
Length:95
Mass (Da):11,163
Last modified:October 1, 1994 - v1
Checksum:iC23856268CEE92E2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77291 Genomic DNA. Translation: CAA54505.1.
Z35787 Genomic DNA. Translation: CAA84845.1.
BK006936 Genomic DNA. Translation: DAA07094.1.
PIRiS45760.
RefSeqiNP_009527.1. NM_001178266.1.

Genome annotation databases

EnsemblFungiiYBL026W; YBL026W; YBL026W.
GeneIDi852255.
KEGGisce:YBL026W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77291 Genomic DNA. Translation: CAA54505.1.
Z35787 Genomic DNA. Translation: CAA84845.1.
BK006936 Genomic DNA. Translation: DAA07094.1.
PIRiS45760.
RefSeqiNP_009527.1. NM_001178266.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70B2-95[»]
4C92X-ray2.30B2-95[»]
4M75X-ray2.95B/I1-95[»]
4M77X-ray3.11B/I1-95[»]
4M78X-ray2.79B/I1-95[»]
4M7AX-ray2.78B/I1-95[»]
4M7DX-ray2.60B/I1-95[»]
4N0AX-ray3.15C/D/G1-95[»]
ProteinModelPortaliP38203.
SMRiP38203. Positions 2-95.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32672. 92 interactions.
DIPiDIP-794N.
IntActiP38203. 65 interactions.
MINTiMINT-383549.

Proteomic databases

MaxQBiP38203.
PaxDbiP38203.
PeptideAtlasiP38203.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBL026W; YBL026W; YBL026W.
GeneIDi852255.
KEGGisce:YBL026W.

Organism-specific databases

CYGDiYBL026w.
EuPathDBiFungiDB:YBL026W.
SGDiS000000122. LSM2.

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00390000016597.
HOGENOMiHOG000166937.
InParanoidiP38203.
KOiK12621.
OMAiDCTLLQD.
OrthoDBiEOG7PZSB0.

Enzyme and pathway databases

BioCyciYEAST:G3O-28929-MONOMER.
ReactomeiREACT_294700. mRNA Splicing - Minor Pathway.

Miscellaneous databases

NextBioi970835.
PROiP38203.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR016654. U6_snRNA_Lsm2.
[Graphical view]
PANTHERiPTHR13829. PTHR13829. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF016394. U6_snRNA_Lsm2. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Analysis of a 17.4 kb DNA segment of yeast chromosome II encompassing the ribosomal protein L19 as well as proteins with homologies to components of the hnRNP and snRNP complexes and to the human proliferation-associated p120 antigen."
    van Dyck L., Jonniaux J.-L., Barreiros T.D.M., Kleine K., Goffeau A.
    Yeast 10:1663-1673(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Complete DNA sequence of yeast chromosome II."
    Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
    , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
    EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin."
    Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.
    EMBO J. 18:3451-3462(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION WITH PRE-P RNA.
  5. "Characterization of Sm-like proteins in yeast and their association with U6 snRNA."
    Mayes A.E., Verdone L., Legrain P., Beggs J.D.
    EMBO J. 18:4321-4331(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  6. "Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP."
    Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R., Fabrizio P.
    EMBO J. 18:4535-4548(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  7. "A Sm-like protein complex that participates in mRNA degradation."
    Bouveret E., Rigaut G., Shevchenko A., Wilm M., Seraphin B.
    EMBO J. 19:1661-1671(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE LSM1-LSM7 COMPLEX, ASSOCIATION OF THE LSM1-LSM7 COMPLEX WITH PAT1 AND XRN1, FUNCTION OF THE LSM1-LSM7 COMPLEX, IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION OF THE LSM2-LSM8 COMPLEX WITH U6 SNRNA, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p."
    Kufel J., Allmang C., Verdone L., Beggs J.D., Tollervey D.
    Mol. Cell. Biol. 22:5248-5256(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSING OF PRE-TRNAS.
  9. "Lsm Proteins are required for normal processing and stability of ribosomal RNAs."
    Kufel J., Allmang C., Petfalski E., Beggs J.D., Tollervey D.
    J. Biol. Chem. 278:2147-2156(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSING OF PRE-RRNAS.
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "A complex pathway for 3' processing of the yeast U3 snoRNA."
    Kufel J., Allmang C., Verdone L., Beggs J., Tollervey D.
    Nucleic Acids Res. 31:6788-6797(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSING OF U3 SNORNA.
  12. "Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex."
    Kufel J., Bousquet-Antonelli C., Beggs J.D., Tollervey D.
    Mol. Cell. Biol. 24:9646-9657(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE LSM2-LSM8 COMPLEX IN NUCLEAR MRNA DEGRADATION.
  13. "Architecture of the Lsm1-7-Pat1 complex: a conserved assembly in eukaryotic mRNA turnover."
    Sharif H., Conti E.
    Cell Rep. 5:283-291(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 27-172 OF LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
  14. "Crystal structure and biochemical analysis of the heptameric Lsm1-7 complex."
    Zhou L., Zhou Y., Hang J., Wan R., Lu G., Yan C., Shi Y.
    Cell Res. 24:497-500(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF LSM1-LSM7 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-63.
  15. "Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation."
    Wu D., Muhlrad D., Bowler M.W., Jiang S., Liu Z., Parker R., Song H.
    Cell Res. 24:233-246(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.15 ANGSTROMS), SUBUNIT, INTERACTION WITH PAT1, FUNCTION, RNA-BINDING.
  16. "Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA."
    Zhou L., Hang J., Zhou Y., Wan R., Lu G., Yin P., Yan C., Shi Y.
    Nature 506:116-120(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF PHE-35; ASN-37 AND ARG-63.

Entry informationi

Entry nameiLSM2_YEAST
AccessioniPrimary (citable) accession number: P38203
Secondary accession number(s): D6VPX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: July 22, 2015
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2210 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.